The following lines from the manual are giving me problems.
>>> params_list = Vector1('ATP.params')
>>> res_set=generate_nonstandard_residue_set(params_list)
This results in an error
ERROR: Cannot find file 'A'
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 147
RuntimeError: unidentifiable C++ exception
If I rename ATP.params to A, and put it in my home directory it finds it.
It looks like a miscommunication passing the string.
Post Situation:
This is just a syntax thing. You need to pass a list to Vector1(), so it should be:
>>> params_list = Vector1(['ATP.params'])
with brackets.
Since you didn't use brackets, it interprets the whole string as a list of characters; hence it looking for a file called "A".
Let us know if this still does not work.
Try using an explicit Vector1_string and making sure you are passing it a list:
params_paths = utility.vector1_string()
params_paths.extend(list(params.keys()))
residuetypeset = generate_nonstandard_residue_set(params_paths)
Vector1(['ATP.params'])
That did it, thanks.